Docker image for the GATB-pipeline assembler
You can take example from the following commands to build and run the GATB-pipeline assembler container.
To build the docker image:
docker build -t gatb/gatb-pipeline .
Then define the following 2 directories:
export dir1=... # where your input data are located on the host machine # (this directory will be mounted inside the container # as /inputs) export dir2=... # where you want to mount the container run directory # on your host machine (for runtime monitoring)
Finally, launch the run:
docker run -it --rm -v $dir1:/inputs -v $dir2:/tmp/gatb-pipeline gatb/gatb-pipeline SRR531199 /inputs /tmp/gatb-pipeline
where SRR531199 is the codename of your experiment (see Procfile).